Sponsored Content
Top Forums UNIX for Advanced & Expert Users Help optimizing sort of large files Post 302925640 by kogorman3 on Tuesday 18th of November 2014 11:13:36 AM
Old 11-18-2014
Quote:
Originally Posted by Corona688
It doesn't work that way. It doesn't run 16384 individual merges simultaneously, then 4096 merges simultaneously, then 1024, etc etc. It always does the number you tell it to, as many times as it takes to process the list of things to do.
That makes no sense to me. If I tell it to make 1GB temporaries, my 13GB test file will make 13 of them and probably merge just once. If I tell it to make 1MB temporaries, it will make 13,000 of them, and likely have to merge the outputs of the first set of merges at least one extra time, handling the same data more times with more disk I/O.

My real TB-sized inputs will see this even more.

BTW, on skimming the sort source code, I found that by default it tries to make the buffer-size parameter 1/8 of physical memory: 4GB. That was so slow that I started this investigation. Smaller turned out to be better, possibly because none of the TLB or caches could deal with it effectively during the initial in-RAM merges because of the huge working set.

Quote:
I don't think small sorts hurt you, especially since they're small enough to be cached. What hurts you are merges on too many files at once for the disk to seek between, reducing it's I/O throughput.

Remember you are trying to find a "sweet spot" where CPU use and disk throughput are both at peak -- where the system can sustain full disk and cpu use.
Not sure what you mean about small sorts; I can't have them. I have large files, requiring large sorts. The files are large enough that I do not expect anything from previous merges to be available if the data has to be merged again, and I expect the data from different inputs to be far enough apart on disk to require seeks no matter what I do. Accordingly, I'd like to minimize the number of merge passes.

Even with these large sizes, sweet spots are exactly what I'm looking for.

Quote:
Check if you're eating into swap sometimes. Hitting swap could have severe performance penalties that throw off your tests.
I'm looking. But with the modest parameters I'm giving it, I hardly expect my 32-GB RAM to need to swap. The largest buffer-size I've ever tried is 4g, and that was already a bad idea and I don't do that any more. I'm distinctly sub-G now.
 

10 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

Large files

I am trying to understand the webserver log file for an error which has occured on my live web site. The webserver access file is very big in size so it's not possible to open this file using vi editor. I know the approximate time the error occured, so i am interested in looking for the log file... (4 Replies)
Discussion started by: sehgalniraj
4 Replies

2. Shell Programming and Scripting

Large Text Files

Hi All I have approximately 10 files that are at least 100+ MB in size. I am importing them into a DB to output them to the web. What i need to do first is clean the files up so i dont have un necessary rows in the DB. Below is what the file looks like: Ignore the <TAB> annotations as that... (4 Replies)
Discussion started by: caddyjoe77
4 Replies

3. UNIX for Dummies Questions & Answers

large files?

How do we check 'large files' is enabled on a Unix box -- HP-UX B11.11 (2 Replies)
Discussion started by: ranj@chn
2 Replies

4. UNIX for Dummies Questions & Answers

Sort large file

I was wondering how sort works. Does file size and time to sort increase geometrically? I have a 5.3 billion line file I'd like to use with sort -u I'm wondering if that'll take forever because of a geometric expansion? If it takes 100 hours that's fine but not 100 days. Thanks so much. (2 Replies)
Discussion started by: dcfargo
2 Replies

5. Shell Programming and Scripting

a problem with large files

hello all, kindly i need your help, i made a script to print a specific lines from a huge file about 3 million line. the output of the script will be about 700,000 line...the problem is the script is too slow...it kept working for 5 days and the output was only 200,000 lines !!! the script is... (16 Replies)
Discussion started by: m_wassal
16 Replies

6. Shell Programming and Scripting

Divide large data files into smaller files

Hello everyone! I have 2 types of files in the following format: 1) *.fa >1234 ...some text... >2345 ...some text... >3456 ...some text... . . . . 2) *.info >1234 (7 Replies)
Discussion started by: ad23
7 Replies

7. UNIX for Dummies Questions & Answers

Speeding/Optimizing GREP search on CSV files

Hi all, I have problem with searching hundreds of CSV files, the problem is that search is lasting too long (over 5min). Csv files are "," delimited, and have 30 fields each line, but I always grep same 4 fields - so is there a way to grep just those 4 fields to speed-up search. Example:... (11 Replies)
Discussion started by: Whit3H0rse
11 Replies

8. Solaris

How to safely copy full filesystems with large files (10Gb files)

Hello everyone. Need some help copying a filesystem. The situation is this: I have an oracle DB mounted on /u01 and need to copy it to /u02. /u01 is 500 Gb and /u02 is 300 Gb. The size used on /u01 is 187 Gb. This is running on solaris 9 and both filesystems are UFS. I have tried to do it using:... (14 Replies)
Discussion started by: dragonov7
14 Replies

9. UNIX for Advanced & Expert Users

Script to sort the files and append the extension .sort to the sorted version of the file

Hello all - I am to this forum and fairly new in learning unix and finding some difficulty in preparing a small shell script. I am trying to make script to sort all the files given by user as input (either the exact full name of the file or say the files matching the criteria like all files... (3 Replies)
Discussion started by: pankaj80
3 Replies

10. Shell Programming and Scripting

Script to sort large file with frequency

Hello, I have a very large file of around 2 million records which has the following structure: I have used the standard awk program to sort: # wordfreq.awk --- print list of word frequencies { # remove punctuation #gsub(/_]/, "", $0) for (i = 1; i <= NF; i++) freq++ } END { for (word... (3 Replies)
Discussion started by: gimley
3 Replies
GIT-MERGE-INDEX(1)						    Git Manual							GIT-MERGE-INDEX(1)

NAME
git-merge-index - Run a merge for files needing merging SYNOPSIS
git merge-index [-o] [-q] <merge-program> (-a | [--] <file>*) DESCRIPTION
This looks up the <file>(s) in the index and, if there are any merge entries, passes the SHA-1 hash for those files as arguments 1, 2, 3 (empty argument if no file), and <file> as argument 4. File modes for the three files are passed as arguments 5, 6 and 7. OPTIONS
-- Do not interpret any more arguments as options. -a Run merge against all files in the index that need merging. -o Instead of stopping at the first failed merge, do all of them in one shot - continue with merging even when previous merges returned errors, and only return the error code after all the merges. -q Do not complain about a failed merge program (a merge program failure usually indicates conflicts during the merge). This is for porcelains which might want to emit custom messages. If git merge-index is called with multiple <file>s (or -a) then it processes them in turn only stopping if merge returns a non-zero exit code. Typically this is run with a script calling Git's imitation of the merge command from the RCS package. A sample script called git merge-one-file is included in the distribution. ALERT ALERT ALERT! The Git "merge object order" is different from the RCS merge program merge object order. In the above ordering, the original is first. But the argument order to the 3-way merge program merge is to have the original in the middle. Don't ask me why. Examples: torvalds@ppc970:~/merge-test> git merge-index cat MM This is MM from the original tree. # original This is modified MM in the branch A. # merge1 This is modified MM in the branch B. # merge2 This is modified MM in the branch B. # current contents or torvalds@ppc970:~/merge-test> git merge-index cat AA MM cat: : No such file or directory This is added AA in the branch A. This is added AA in the branch B. This is added AA in the branch B. fatal: merge program failed where the latter example shows how git merge-index will stop trying to merge once anything has returned an error (i.e., cat returned an error for the AA file, because it didn't exist in the original, and thus git merge-index didn't even try to merge the MM thing). GIT
Part of the git(1) suite Git 1.8.3.1 06/10/2014 GIT-MERGE-INDEX(1)
All times are GMT -4. The time now is 05:36 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy